As an X-Phile, I'm forced to admit that what intrigued me most about this film is its plot's resemblance to one of my favorite X-Files episodes: Milagro.
Milagro actually told 2 stories. There was (1) a writer with the power to murder through his "fiction," and (2) the real-life writer the Milagro character symbolized, Chris Carter, who learned that his characters had spawned a life of their own and could no longer follow the direction that he'd planned for them.
Of course, in Stranger Than Fiction, the writer, Karen Eiffel, does not exactly lose control of her characters against her will, as is the case in Milagro. In fact, her protagonist is prepared to submit to his fate. And he does so, not because he concludes he has no control over his actions, upon learning that he exists only in a writer's head, but because he decides that the course the writer has fated for him is actually the best one, for reasons bigger than himself.
Faced with the humanity and humanness of the man she conceived in ink, Eiffel herself must also define (or redefine) what the "greater good" really is and she changes her plot, not because she had no choice or lost control, but because power possessed need not always be power exercised.
In this way, Eiffel learned a lesson that eluded both the Milagro killer and the man responsible for him (Chris Carter). I don't think Carter ever became reconciled to the fact that his vision of Mulder and Scully had to give way to what the fans', actors' and network "suits'" inexorable influence on the X-Files became. Carter didn't change his course, so much as he was driven off the road. Likewise, the Milagro writer (Padgett) learns that while the pen is greater than the sword, love is greater than his pen. He does not relinquish his vision as author, but is blinded and has it taken from him. Conversely, Eiffel is never defeated as a writer. She just learns that there is more than one way (and more than one reason) to tell a story.
In crafting her novel, Eiffel was never looking for fame and fortune or even artistic pleasure. She only sought literary perfection. But she realized characters so lifelike that ultimately she decided that even if it's only on paper, she had no right to play God.